[gmx-users] Check point file

[Dallas Warren]

Note the .cpt file is a snap shot file, like a .gro coordinate file.
It saves the state of the system at a particular point of time in a
manner that you can have an exact restart at that time.

You can still continue from 80ns relatively closely using the
appropriate files you already have, you are not starting a "brand new"
simulation. You can also join together the trajectory and energy files
once it is completed.

gmx grompp -f 400Kfor20ns.mdp -p topol.top -c 80ns.gro -e 0-80ns.edr
-o continuation.tpr
gmx mdrun -s continuation.tpr


Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Tue, 25 Jun 2019 at 01:08, Alex <alexanderwien2k at gmail.com> wrote:
>
> Hi Mark
> Actually the simulation I am talking about is an annealing simulation in
> which the system are being annealed from room temperature to 400 k during a
> 80 ns simulation and then the temperature are being ramped down again to be
> at room temperature at 100 ns. Now I just want to keep continuing the
> annealing from 80 ns (keeping the temperature at 400 k) instead of ramping
> down. And If I start a completely brand new simulation the way you
> mentioned, it does not continue the simulation at the annealed temperature
> of my previous simulation.
> I wish the state.cpt was also truncate-able likes the xtc and trr files to
> have all at 80 ns.
>
> Regards,
> Alex
>
> On Mon, Jun 24, 2019 at 5:41 AM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > On Mon., 24 Jun. 2019, 11:21 Alex, <alexanderwien2k at gmail.com> wrote:
> >
> > > Thanks Mark.
> > > With not be able to append to the simulation files, you mean, I should
> > not
> > > use the "-cpi state.cpt" in the gmx mdrun, right?
> >
> >
> > No, I mean you can't use -append. You have no relevant file for -cpi.
> >
> > > If
> >
> > > so, then, the
> > > simulation is a completely brand new simulation excepts that it use -c
> > > case.80ns.gro file as starting frame from t = 0.0. Then does the
> > > trjcat/eneconv used for later concatenation know that the new outputs
> > > should be assigned to the time t = 8000*1*?
> > >
> >
> > The link I gave earlier has hints for how to prepare for this to go
> > smoothly.
> >
> > In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything
> > > are being continued from t = 100000.
> > >
> >
> > Yes
> >
> > Mark
> >
> >
> > > Thank you.
> > > Alex
> > >
> > > On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham <mark.j.abraham at gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > No, that isn't meaningful. Follow
> > > >
> > > >
> > >
> > http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart
> > > > but
> > > > for the -c option, pass a file containing the desired frame extracted
> > > from
> > > > your .trr file. You will not be able to append to the simulation files,
> > > but
> > > > once the simulation is complete, you can concatenate all the files with
> > > > trjcat/eneconv.
> > > >
> > > > Mark
> > > >
> > > > On Sun, 23 Jun 2019 at 22:53, Alex <alexanderwien2k at gmail.com> wrote:
> > > >
> > > > > Dear all,
> > > > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr,
> > > > > case.100ns.cpt ... all are here,  I want to truncate the xtc file at
> > 80
> > > > ns
> > > > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr
> > file.
> > > > > Everything is clear for me except the case.cpt file for which is not
> > > > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr.
> > > > > So, I wonder if it is meaningful if I use the case.100ns.cpt,,
> > > > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point?
> > > > >
> > > > > Thank you.
> > > > > Alex
> > > > > --
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